X-49191526-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_003179.3(SYP):c.853G>A(p.Gly285Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000661 in 1,210,067 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003179.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SYP | NM_003179.3 | c.853G>A | p.Gly285Ser | missense_variant | 6/7 | ENST00000263233.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SYP | ENST00000263233.9 | c.853G>A | p.Gly285Ser | missense_variant | 6/7 | 1 | NM_003179.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000886 AC: 1AN: 112832Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35056
GnomAD3 exomes AF: 0.0000113 AC: 2AN: 177753Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 64535
GnomAD4 exome AF: 0.00000638 AC: 7AN: 1097235Hom.: 0 Cov.: 31 AF XY: 0.00000827 AC XY: 3AN XY: 362867
GnomAD4 genome ? AF: 0.00000886 AC: 1AN: 112832Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35056
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 01, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at